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D

David M. McCandlish

Simons Center for Quantitative Biology

23H-index
97Paper Count
2.6KCitation Count
Published Papers 32
Publication Date
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Gaugefixer: overcoming parameter non-identifiability in models of sequence-function relationships
errBMC Bioinformatics
IF3.3
err2026-08-22
err0
errOAAI
errCarlos Martí-Gómez; David M. McCandlish; Justin B. Kinney
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On learning functions over biological sequence space: relating Gaussian process priors, regularization, and gauge fixing
errJournal of Mathematical Biology
IF2.3
err2026-04-29
err0
PREAI
errPetti, Samantha; Marti-Gomez, Carlos; Kinney, Justin B.; Zhou, Juannan; McCandlish, David M.
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Inference and Visualization of Complex Genotype-Phenotype Maps
errMolecular Biology and Evolution
IF5.3
err2026-02-01
err1
PREAI
errMarti-Gomez, Carlos; Zhou, Juannan; Chen, Wei-Chia; Stoltzfus, Arlin; Kinney, Justin B.; McCandlish, David M.
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A side-by-side comparison of variant function measurements using deep mutational scanning and base editing
errNUCLEIC ACIDS RESEARCH
IF13.1
err2025-08-12
err0
errOAAI
errSokirniy, Ivan; Inam, Haider; Tomaszkiewicz, Marta; Reynolds, Joshua; McCandlish, David; Pritchard, Justin
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Cryptic variation fuels plant phenotypic change through hierarchical epistasis
errNature
IF48.5
err2025-07-09
err0
errOAAI
errSophia G. Zebell; Carlos Martí-Gómez; Blaine Fitzgerald; Camila P. Cunha; Michael Lach; Brooke M. Seman; Anat Hendelman; Simon Sretenovic; Yiping Qi; Madelaine Bartlett; Yuval Eshed; David M. McCandlish; Zachary B. Lippman
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errSave
Guidelines for releasing a variant effect predictor
errGENOME BIOLOGY
IF9.4
err2025-04-15
err1
errOAAI
errLivesey, Benjamin J.; Badonyi, Mihaly; Dias, Mafalda; Frazer, Jonathan; Kumar, Sushant; Lindorff-Larsen, Kresten; Mccandlish, David M.; Orenbuch, Rose; Shearer, Courtney A.; Muffley, Lara; Foreman, Julia; Glazer, Andrew M.; Lehner, Ben; Marks, Debora S.; Roth, Frederick P.; Rubin, Alan F.; Starita, Lea M.
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Symmetry, gauge freedoms, and the interpretability of sequence-function relationships
errPHYSICAL REVIEW RESEARCH
IF4.2
err2025-04-02
err0
errOAAI
errPosfai, Anna; Mccandlish, David M.; Kinney, Justin B.
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errSave
Gauge fixing for sequence-function relationships
errplos biology
IF3.6
err2025-03-20
err1
errOAAI
errPosfai, Anna; Zhou, Juannan; McCandlish, David M.; Kinney, Justin B.
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errSave
Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes in Caenorhabditis elegans
errNATURE COMMUNICATIONS
IF15.7
err2024-09-19
err0
errOAAI
errGitschlag, Bryan L.; Pereira, Claudia V.; Held, James P.; McCandlish, David M.; Patel, Maulik R.
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Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models
errNATURE MACHINE INTELLIGENCE
IF23.9
err2024-06-21
err5
PREAI
errSeitz, Evan E.; Mccandlish, David M.; Kinney, Justin B.; Koo, Peter K.
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Specificity, synergy, and mechanisms of splice-modifying drugs
errNATURE COMMUNICATIONS
IF15.7
err2024-02-29
err6
errOAAI
errIshigami, Yuma; Wong, Mandy S.; Marti-Gomez, Carlos; Ayaz, Andalus; Kooshkbaghi, Mahdi; Hanson, Sonya M.; Mccandlish, David M.; Krainer, Adrian R.; Kinney, Justin B.
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errSave
Designed active-site library reveals thousands of functional GFP variants
errNATURE COMMUNICATIONS
IF15.7
err2023-05-20
err12
errOAAI
errWeinstein, Jonathan Yaacov; Marti-Gomez, Carlos; Lipsh-Sokolik, Rosalie; Hoch, Shlomo Yakir; Liebermann, Demian; Nevo, Reinat; Weissman, Haim; Petrovich-Kopitman, Ekaterina; Margulies, David; Ivankov, Dmitry; McCandlish, David M.; Fleishman, Sarel J.
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Mutation bias and the predictability of evolution
errPHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
IF4.7
err2023-04-03
err14
errOAAI
errCano, Alejandro V.; Gitschlag, Bryan L.; Rozhonova, Hana; Stoltzfus, Arlin; McCandlish, David M.; Payne, Joshua L.
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MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect
errGENOME BIOLOGY
IF9.4
err2022-04-15
err9
errOAAI
errTareen, Ammar; Kooshkbaghi, Mahdi; Posfai, Anna; Ireland, William T.; McCandlish, David M.; Kinney, Justin B.
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errSave
Mutation bias shapes the spectrum of adaptive substitutions
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2022-02-10
err25
errOAAI
errCano, Alejandro V.; Rozhonova, Hana; Stoltzfus, Arlin; McCandlish, David M.; Payne, Joshua L.
errShare
errSave
System-specificity of genotype-phenotype map structure Comment on From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics by Susanna Manrubia et al.
errPHYSICS OF LIFE REVIEWS
IF14.3
err2021-12-01
err1
PREAI
errMcCandlish, David M.
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errSave
Field-theoretic density estimation for biological sequence space with applications to 5' splice site diversity and aneuploidy in cancer
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2021-10-01
err3
errOAAI
errChen, Wei-Chia; Zhou, Juannan; Sheltzer, Jason M.; Kinney, Justin B.; McCandlish, David M.
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errSave
Minimum epistasis interpolation for sequence-function relationships
errNATURE COMMUNICATIONS
IF15.7
err2020-04-14
err14
errOAAI
errZhou, Juannan; McCandlish, David M.
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Massively Parallel Assays and Quantitative Sequence-Function Relationships
errANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, VOL 20, 2019
IF0
err2019-08-31
err96
errOAAI
errKinney, Justin B.; McCandlish, David M.
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errSave
The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function
errPHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
IF4.7
err2019-06-03
err33
errOAAI
errStorz, Jay F.; Natarajan, Chandrasekhar; Signore, Anthony V.; Witt, Christopher C.; McCandlish, David M.; Stoltzfus, Arlin
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Research Directions

No research directions
Co-authors
Cooperation Journals
F
Frederick P. Roth
H-index: 79 · Papers: 276
K
Kresten Lindorff‐Larsen
H-index: 70 · Papers: 763
D
Debora S. Marks
H-index: 66 · Papers: 249
Y
Yuval Eshed
H-index: 65 · Papers: 108
J
Joshua B. Plotkin
H-index: 64 · Papers: 278
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